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<b>An Object Oriented Finite Element Library</b></font></p>
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<div class="header">
  <div class="summary">
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#friends">Friends</a> &#124;
<a href="classOFELI_1_1PETScWrapper-members.html">List of all members</a>  </div>
  <div class="headertitle">
<div class="title">PETScWrapper&lt; T_ &gt; Class Template Reference<div class="ingroups"><a class="el" href="group__OFELI.html">OFELI</a><a class="el" href="group__OFELI.html">OFELI</a> &raquo;  &#124; <a class="el" href="group__VectMat.html">Vector and Matrix</a></div></div>  </div>
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<p>This class is a wrapper to be used when the library Petsc is installed and used with <a class="el" href="namespaceOFELI.html" title="A namespace to group all library classes, functions, ... ">OFELI</a>.  
 <a href="classOFELI_1_1PETScWrapper.html#details">More...</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:acca1b3684c9b592d1a86fa31caa647cd"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#acca1b3684c9b592d1a86fa31caa647cd">PETScWrapper</a> (int argc, char **args, string help=&quot;&quot;)</td></tr>
<tr class="memdesc:acca1b3684c9b592d1a86fa31caa647cd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor with program arguments.  <a href="#acca1b3684c9b592d1a86fa31caa647cd">More...</a><br /></td></tr>
<tr class="separator:acca1b3684c9b592d1a86fa31caa647cd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1a4ca5f4f158dab1589828302501e4eb"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a1a4ca5f4f158dab1589828302501e4eb">~PETScWrapper</a> ()</td></tr>
<tr class="memdesc:a1a4ca5f4f158dab1589828302501e4eb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Destructor.  <a href="#a1a4ca5f4f158dab1589828302501e4eb">More...</a><br /></td></tr>
<tr class="separator:a1a4ca5f4f158dab1589828302501e4eb"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a838c9bd3b28e805c82eb99ed28446b10"><td class="memItemLeft" align="right" valign="top">PetscErrorCode&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a838c9bd3b28e805c82eb99ed28446b10">getIntOption</a> (string s, PetscInt &amp;n, PetscBool &amp;set) const </td></tr>
<tr class="memdesc:a838c9bd3b28e805c82eb99ed28446b10"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an option as an integer number.  <a href="#a838c9bd3b28e805c82eb99ed28446b10">More...</a><br /></td></tr>
<tr class="separator:a838c9bd3b28e805c82eb99ed28446b10"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:abaa8b67ef1490eef726cc0fc0698a567"><td class="memItemLeft" align="right" valign="top">PetscErrorCode&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#abaa8b67ef1490eef726cc0fc0698a567">getBoolOption</a> (string s, PetscBool &amp;<a class="el" href="group__OFELI.html#gaf5cd2eaaceda19772fd904539819158c">b</a>, PetscBool &amp;set) const </td></tr>
<tr class="memdesc:abaa8b67ef1490eef726cc0fc0698a567"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get an option as a bool variable.  <a href="#abaa8b67ef1490eef726cc0fc0698a567">More...</a><br /></td></tr>
<tr class="separator:abaa8b67ef1490eef726cc0fc0698a567"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a04f269cf03f6e555894587336fce9da3"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a04f269cf03f6e555894587336fce9da3"></a>
PetscMPIInt&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a04f269cf03f6e555894587336fce9da3">size</a> () const </td></tr>
<tr class="memdesc:a04f269cf03f6e555894587336fce9da3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Return wrapper size, <em>i.e.</em> number of processors. <br /></td></tr>
<tr class="separator:a04f269cf03f6e555894587336fce9da3"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a183a0f831838eaca359bbdfcd0747f80"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a183a0f831838eaca359bbdfcd0747f80">setMesh</a> (<a class="el" href="classOFELI_1_1Mesh.html">Mesh</a> &amp;ms)</td></tr>
<tr class="memdesc:a183a0f831838eaca359bbdfcd0747f80"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set mesh.  <a href="#a183a0f831838eaca359bbdfcd0747f80">More...</a><br /></td></tr>
<tr class="separator:a183a0f831838eaca359bbdfcd0747f80"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad55999723924ca14c1364e1924b26980"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#ad55999723924ca14c1364e1924b26980">setPartition</a> (<a class="el" href="classOFELI_1_1Partition.html">Partition</a> &amp;p)</td></tr>
<tr class="memdesc:ad55999723924ca14c1364e1924b26980"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set mesh partition.  <a href="#ad55999723924ca14c1364e1924b26980">More...</a><br /></td></tr>
<tr class="separator:ad55999723924ca14c1364e1924b26980"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aafd580685957ff020c6265c8304c41d5"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#aafd580685957ff020c6265c8304c41d5">setMatrix</a> (<a class="el" href="classOFELI_1_1PETScMatrix.html">PETScMatrix</a>&lt; T_ &gt; &amp;<a class="el" href="group__OFELI.html#ga8d83ae0344b0fbb3265762cd97e1b1db">A</a>)</td></tr>
<tr class="memdesc:aafd580685957ff020c6265c8304c41d5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Define problem matrix.  <a href="#aafd580685957ff020c6265c8304c41d5">More...</a><br /></td></tr>
<tr class="separator:aafd580685957ff020c6265c8304c41d5"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a294563b2d70e552d6b6a081651f91c36"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a294563b2d70e552d6b6a081651f91c36">setLinearSystem</a> (<a class="el" href="classOFELI_1_1PETScMatrix.html">PETScMatrix</a>&lt; T_ &gt; &amp;<a class="el" href="group__OFELI.html#ga8d83ae0344b0fbb3265762cd97e1b1db">A</a>, <a class="el" href="classOFELI_1_1PETScVect.html">PETScVect</a>&lt; T_ &gt; &amp;<a class="el" href="group__OFELI.html#gaf5cd2eaaceda19772fd904539819158c">b</a>, string s=KSPCG, string p=PCJACOBI, <a class="el" href="group__Util.html#gaccfeb6b1e8cf41731fde610549bee67c">real_t</a> tol=1.e-12, size_t max_it=1000)</td></tr>
<tr class="memdesc:a294563b2d70e552d6b6a081651f91c36"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set linear system features.  <a href="#a294563b2d70e552d6b6a081651f91c36">More...</a><br /></td></tr>
<tr class="separator:a294563b2d70e552d6b6a081651f91c36"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a2539d5d0156f9dada9c35d78a12ee9fd"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a2539d5d0156f9dada9c35d78a12ee9fd">setPreconditioner</a> (string p)</td></tr>
<tr class="memdesc:a2539d5d0156f9dada9c35d78a12ee9fd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Choose preconditioner for the iterative procedure.  <a href="#a2539d5d0156f9dada9c35d78a12ee9fd">More...</a><br /></td></tr>
<tr class="separator:a2539d5d0156f9dada9c35d78a12ee9fd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:afde2af238762523b878bd5a94506adb4"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#afde2af238762523b878bd5a94506adb4">setIterationParameters</a> (<a class="el" href="group__Util.html#gaccfeb6b1e8cf41731fde610549bee67c">real_t</a> tol, size_t max_it)</td></tr>
<tr class="memdesc:afde2af238762523b878bd5a94506adb4"><td class="mdescLeft">&#160;</td><td class="mdescRight">Choose iteration parameters.  <a href="#afde2af238762523b878bd5a94506adb4">More...</a><br /></td></tr>
<tr class="separator:afde2af238762523b878bd5a94506adb4"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab26be02833420714637713f657452033"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#ab26be02833420714637713f657452033">setIterationMethod</a> (string m)</td></tr>
<tr class="memdesc:ab26be02833420714637713f657452033"><td class="mdescLeft">&#160;</td><td class="mdescRight">Choose the iterative method.  <a href="#ab26be02833420714637713f657452033">More...</a><br /></td></tr>
<tr class="separator:ab26be02833420714637713f657452033"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa31ed509b117f392ae868a5639e40b97"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#aa31ed509b117f392ae868a5639e40b97">solve</a> (<a class="el" href="classOFELI_1_1PETScVect.html">PETScVect</a>&lt; T_ &gt; &amp;x)</td></tr>
<tr class="memdesc:aa31ed509b117f392ae868a5639e40b97"><td class="mdescLeft">&#160;</td><td class="mdescRight">Solve the linear system.  <a href="#aa31ed509b117f392ae868a5639e40b97">More...</a><br /></td></tr>
<tr class="separator:aa31ed509b117f392ae868a5639e40b97"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a08de4952108b7adaae510d91a299d20e"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a08de4952108b7adaae510d91a299d20e">solve</a> (const <a class="el" href="classOFELI_1_1PETScVect.html">PETScVect</a>&lt; T_ &gt; &amp;<a class="el" href="group__OFELI.html#gaf5cd2eaaceda19772fd904539819158c">b</a>, <a class="el" href="classOFELI_1_1PETScVect.html">PETScVect</a>&lt; T_ &gt; &amp;x)</td></tr>
<tr class="memdesc:a08de4952108b7adaae510d91a299d20e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Solve the linear system.  <a href="#a08de4952108b7adaae510d91a299d20e">More...</a><br /></td></tr>
<tr class="separator:a08de4952108b7adaae510d91a299d20e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aaf95920bd6f26d0e910751f15b0e5d3c"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#aaf95920bd6f26d0e910751f15b0e5d3c">checkError</a> (<a class="el" href="classOFELI_1_1PETScVect.html">PETScVect</a>&lt; T_ &gt; &amp;u) const </td></tr>
<tr class="memdesc:aaf95920bd6f26d0e910751f15b0e5d3c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Check residual error.  <a href="#aaf95920bd6f26d0e910751f15b0e5d3c">More...</a><br /></td></tr>
<tr class="separator:aaf95920bd6f26d0e910751f15b0e5d3c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1500668d1e915d798a3e35b46a2c552a"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a1500668d1e915d798a3e35b46a2c552a"></a>
int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a1500668d1e915d798a3e35b46a2c552a">getIterationNumber</a> () const </td></tr>
<tr class="memdesc:a1500668d1e915d798a3e35b46a2c552a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Return the number of iterations. <br /></td></tr>
<tr class="separator:a1500668d1e915d798a3e35b46a2c552a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad17a145510f14f3eed5514d21c08b2d6"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#ad17a145510f14f3eed5514d21c08b2d6">setLSTolerances</a> (<a class="el" href="group__Util.html#gaccfeb6b1e8cf41731fde610549bee67c">real_t</a> rel_tol, <a class="el" href="group__Util.html#gaccfeb6b1e8cf41731fde610549bee67c">real_t</a> abs_tol, <a class="el" href="group__Util.html#gaccfeb6b1e8cf41731fde610549bee67c">real_t</a> div_tol=PETSC_DEFAULT, int max_it=PETSC_DEFAULT) const </td></tr>
<tr class="memdesc:ad17a145510f14f3eed5514d21c08b2d6"><td class="mdescLeft">&#160;</td><td class="mdescRight">Set tolerance parameters for a linear system.  <a href="#ad17a145510f14f3eed5514d21c08b2d6">More...</a><br /></td></tr>
<tr class="separator:ad17a145510f14f3eed5514d21c08b2d6"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3736e72b4695cf6264c5845a35a3ad4d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a3736e72b4695cf6264c5845a35a3ad4d"></a>
PetscMPIInt&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a3736e72b4695cf6264c5845a35a3ad4d">getRank</a> () const </td></tr>
<tr class="memdesc:a3736e72b4695cf6264c5845a35a3ad4d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Return the rank of the current processor. <br /></td></tr>
<tr class="separator:a3736e72b4695cf6264c5845a35a3ad4d"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="friends"></a>
Friends</h2></td></tr>
<tr class="memitem:a518d2ad2c711550500e116a8c7107c1d"><td class="memTemplParams" colspan="2"><a class="anchor" id="a518d2ad2c711550500e116a8c7107c1d"></a>
template&lt;class S_ &gt; </td></tr>
<tr class="memitem:a518d2ad2c711550500e116a8c7107c1d"><td class="memTemplItemLeft" align="right" valign="top">ostream &amp;&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOFELI_1_1PETScWrapper.html#a518d2ad2c711550500e116a8c7107c1d">operator&lt;&lt;</a> (ostream &amp;s, const <a class="el" href="classOFELI_1_1PETScWrapper.html">PETScWrapper</a>&lt; S_ &gt; &amp;w)</td></tr>
<tr class="memdesc:a518d2ad2c711550500e116a8c7107c1d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Output wrapper information. <br /></td></tr>
<tr class="separator:a518d2ad2c711550500e116a8c7107c1d"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><h3>template&lt;class T_&gt;<br />
class OFELI::PETScWrapper&lt; T_ &gt;</h3>

<p>This class is a wrapper to be used when the library Petsc is installed and used with <a class="el" href="namespaceOFELI.html" title="A namespace to group all library classes, functions, ... ">OFELI</a>. </p>
<p>When Petsc is used, an instance of class <a class="el" href="classOFELI_1_1PETScWrapper.html" title="This class is a wrapper to be used when the library Petsc is installed and used with OFELI...">PETScWrapper</a> is to be declared. It initializes the use of Petsc and enables calling solver functions in Petsc.</p>
<dl class="tparams"><dt>Template Parameters</dt><dd>
  <table class="tparams">
    <tr><td class="paramname">T_</td><td>Data type (double, int, complex&lt;double&gt;, ...)</td></tr>
  </table>
  </dd>
</dl>
<p>When a linear system is invoked, the choice of iterative solvers can be made among the following methods (see Petsc documentation for more details): </p><ul>
<li>
<code>KSPRICHARDSON</code>: The Richardson iterative method (Default damping parameter is <code>1.0</code>) </li>
<li>
<code>KSPCHEBYSHEV</code>: The Chebyshev iterative method </li>
<li>
<code>KSPCG</code>: The conjugate gradient method [Default] </li>
<li>
<code>KSPCGNE</code>: The CG method for normal equations (without explicitly forming the product <code>A^TA</code> </li>
<li>
<code>KSPGMRES</code>: [Default] The GMRES iterative method (see A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems. Y. Saad and M. H. Schultz, SIAM J. Sci. Stat. Comput., Vo|. 7, No. 3, July 1986, pp. 856-869) </li>
<li>
<code>KSPFGMRES</code>: The Flexible GMRES method (with restart) </li>
<li>
<code>KSPLGMRES</code>: The 'augmented' standard GMRES method where the subspace uses approximations to the error from previous restart cycles </li>
<li>
<code>KSPTCQMR</code>: A variant of QMR (quasi minimal residual) developed by Tony Chan </li>
<li>
<code>KSPBCGS</code>: The BiCGStab (Stabilized version of BiConjugate Gradient Squared) method </li>
<li>
<code>KSPIBCGS</code>: The IBiCGStab (Improved Stabilized version of BiConjugate Gradient Squared) method in an alternative form to have only a single global reduction operation instead of the usual 3 (or 4) </li>
<li>
<code>KSPFBCGS</code>: The flexible BiCGStab method. </li>
<li>
<code>KSPCGS</code>: The CGS (Conjugate Gradient Squared) method </li>
<li>
<code>KSPTFQMR</code>: A transpose free QMR (quasi minimal residual) </li>
<li>
<code>KSPCR</code>: The conjugate residuals method </li>
<li>
<code>KSPLSQR</code>: The LSQR method </li>
<li>
<code>KSPBICG</code>: The Biconjugate gradient method (similar to running the conjugate gradient on the normal equations) </li>
<li>
<code>KSPMINRES</code>: The MINRES (Minimum Residual) method </li>
<li>
<code>KSPSYMMLQ</code>: The SYMMLQ method </li>
<li>
<code>KSPGCR</code>: The Generalized Conjugate Residual method </li>
</ul>
<p>When a linear system is invoked, the choice of a preconditioner can be made among the following methods (see Petsc documentation for more details): </p><ul>
<li>
<code>PCJACOBI</code>: [Default] Jacobi (<em>i.e.</em> diagonal scaling) preconditioning </li>
<li>
<code>PCBJACOBI</code>: Block Jacobi preconditioning, each block is (approximately) solved with its own KSP object </li>
<li>
<code>PCSOR</code>: (S)SOR (successive over relaxation, Gauss-Seidel) preconditioning </li>
<li>
<code>PCEISENSTAT</code>: An implementation of SSOR (symmetric successive over relaxation, symmetric Gauss-Seidel) preconditioning that incorporates Eisenstat's trick to reduce the amount of computation needed </li>
<li>
<code>PCICC</code>: Incomplete Cholesky factorization preconditioners </li>
<li>
<code>PCILU</code>: Incomplete factorization preconditioners </li>
<li>
<code>PCASM</code>: Use the (restricted) additive Schwarz method, each block is (approximately) solved with its own KSP object </li>
<li>
<code>PCLU</code>: Uses a direct solver, based on LU factorization, as a preconditioner </li>
<li>
<code>PCCHOLESKY</code>: Uses a direct solver, based on Cholesky factorization, as a preconditioner </li>
</ul>
</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
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          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>argc</em>, </td>
        </tr>
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          <td class="paramkey"></td>
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          <td class="paramtype">char **&#160;</td>
          <td class="paramname"><em>args</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">string&#160;</td>
          <td class="paramname"><em>help</em> = <code>&quot;&quot;</code>&#160;</td>
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<p>Constructor with program arguments. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">argc</td><td>Count of number of command line arguments </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">args</td><td>The command line arguments. Here is the list of arguments: <ul>
<li>
<code>-start_in_debugger [noxterm,dbx,xdb,gdb,...]</code><ul>
<li>Starts program in debugger </li>
</ul>
</li>
<li>
<code>-on_error_attach_debugger [noxterm,dbx,xdb,gdb,...]</code><ul>
<li>Starts debugger when error detected </li>
</ul>
</li>
<li>
<code>-on_error_emacs &lt;machinename&gt;</code> causes emacsclient to jump to error file<ul>
<li>. -on_error_abort calls abort() when error detected (no traceback) </li>
</ul>
</li>
<li>
<code>-on_error_mpiabort</code> calls MPI_abort() when error detected<ul>
<li>. -error_output_stderr prints error messages to stderr instead of the default stdout </li>
</ul>
</li>
<li>
<code>-error_output_none</code> does not print the error messages (but handles errors in the same way as if this was not called)<ul>
<li>. -debugger_nodes [node1,node2,...] - Indicates nodes to start in debugger </li>
</ul>
</li>
<li>
<code>-debugger_pause [sleeptime]</code> (in seconds)<ul>
<li>Pauses debugger </li>
</ul>
</li>
<li>
<code>-stop_for_debugger</code><ul>
<li>Print message on how to attach debugger manually to process and wait (<code>-debugger_pause</code>) seconds for attachment </li>
</ul>
</li>
<li>
<code>-malloc</code><ul>
<li>Indicates use of PETSc error-checking malloc (on by default for debug version of libraries) </li>
</ul>
</li>
<li>
<code>-malloc no</code><ul>
<li>Indicates not to use error-checking malloc </li>
</ul>
</li>
<li>
<code>-malloc_debug</code><ul>
<li>check for memory corruption at EVERY malloc or free </li>
</ul>
</li>
<li>
<code>-malloc_dump</code><ul>
<li>prints a list of all unfreed memory at the end of the run </li>
</ul>
</li>
<li>
<code>-malloc_test</code><ul>
<li>like <code>-malloc_dump</code> <code>-malloc_debug</code>, but only active for debugging builds </li>
</ul>
</li>
<li>
<code>-fp_trap</code><ul>
<li>Stops on floating point exceptions (Note that on the IBM RS6000 this slows code by at least a factor of 10.) </li>
</ul>
</li>
<li>
<code>-no_signal_handler</code><ul>
<li>Indicates not to trap error signals </li>
</ul>
</li>
<li>
<code>-shared_tmp</code><ul>
<li>indicates <code>/tmp</code> directory is shared by all processors </li>
</ul>
</li>
<li>
<code>-not_shared_tmp</code><ul>
<li>each processor has own <code>/tmp</code> </li>
</ul>
</li>
<li>
<code>-tmp</code><ul>
<li>alternative name of <code>/tmp</code> directory </li>
</ul>
</li>
<li>
<code>-get_total_flops</code><ul>
<li>returns total flops done by all processors </li>
</ul>
</li>
<li>
<code>-memory_info</code><ul>
<li>Print memory usage at end of run </li>
</ul>
</li>
</ul>
</td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">help</td><td>String that contains message to display when argument <code>-v</code> is used</td></tr>
  </table>
  </dd>
</dl>
<dl class="section warning"><dt>Warning</dt><dd>This class is available only when <a class="el" href="namespaceOFELI.html" title="A namespace to group all library classes, functions, ... ">OFELI</a> has been installed with Petsc </dd></dl>

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<p>Destructor. </p>
<p>Destroy the KSP context and release memory allocated by petsc </p>

</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
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          <td class="paramtype">string&#160;</td>
          <td class="paramname"><em>s</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">PetscInt &amp;&#160;</td>
          <td class="paramname"><em>n</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">PetscBool &amp;&#160;</td>
          <td class="paramname"><em>set</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td> const</td>
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<p>Get an option as an integer number. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">s</td><td>String to preprend the name of the option </td></tr>
    <tr><td class="paramdir">[out]</td><td class="paramname">n</td><td>Obtained integer value </td></tr>
    <tr><td class="paramdir">[out]</td><td class="paramname">set</td><td><code>true</code> if found, <code>false</code> if not. </td></tr>
  </table>
  </dd>
</dl>

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          <td class="paramname"><em>s</em>, </td>
        </tr>
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          <td class="paramkey"></td>
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          <td class="paramtype">PetscBool &amp;&#160;</td>
          <td class="paramname"><em>b</em>, </td>
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          <td class="paramkey"></td>
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          <td class="paramtype">PetscBool &amp;&#160;</td>
          <td class="paramname"><em>set</em>&#160;</td>
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<p>Get an option as a bool variable. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">s</td><td>String to preprend the name of the option </td></tr>
    <tr><td class="paramdir">[out]</td><td class="paramname">b</td><td>Obtained boolean value </td></tr>
    <tr><td class="paramdir">[out]</td><td class="paramname">set</td><td><code>true</code> if found, <code>false</code> if not. </td></tr>
  </table>
  </dd>
</dl>

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          <td class="paramtype"><a class="el" href="classOFELI_1_1Mesh.html">Mesh</a> &amp;&#160;</td>
          <td class="paramname"><em>ms</em></td><td>)</td>
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<p>Set mesh. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">ms</td><td><a class="el" href="classOFELI_1_1Mesh.html" title="To store and manipulate finite element meshes. ">Mesh</a> instance </td></tr>
  </table>
  </dd>
</dl>

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          <td>(</td>
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          <td class="paramname"><em>p</em></td><td>)</td>
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<p>Set mesh partition. </p>
<p>This function is to be used for parallel computing </p><dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">p</td><td><a class="el" href="classOFELI_1_1Partition.html" title="To partition a finite element mesh into balanced submeshes. ">Partition</a> instance </td></tr>
  </table>
  </dd>
</dl>

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          <td class="paramname"><em>A</em></td><td>)</td>
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<p>Define problem matrix. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">A</td><td><a class="el" href="classOFELI_1_1PETScMatrix.html" title="To handle matrices in sparse storage format using the Petsc library. ">PETScMatrix</a> instance that contains matrix </td></tr>
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  </dd>
</dl>

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          <td class="paramname"><em>A</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="classOFELI_1_1PETScVect.html">PETScVect</a>&lt; T_ &gt; &amp;&#160;</td>
          <td class="paramname"><em>b</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">string&#160;</td>
          <td class="paramname"><em>s</em> = <code>KSPCG</code>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">string&#160;</td>
          <td class="paramname"><em>p</em> = <code>PCJACOBI</code>, </td>
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        <tr>
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          <td></td>
          <td class="paramtype"><a class="el" href="group__Util.html#gaccfeb6b1e8cf41731fde610549bee67c">real_t</a>&#160;</td>
          <td class="paramname"><em>tol</em> = <code>1.e-12</code>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>max_it</em> = <code>1000</code>&#160;</td>
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<p>Set linear system features. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">A</td><td><a class="el" href="classOFELI_1_1PETScMatrix.html" title="To handle matrices in sparse storage format using the Petsc library. ">PETScMatrix</a> instance that contains matrix </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">b</td><td>Vector containing the right-hand side </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">s</td><td>Option to choose iterative solver. See the definition of the class for iterative methods </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">p</td><td>Option to choose preconditioner. See the definition of the class for available preconditioners. </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">tol</td><td>Tolerance for convergence of iteration process [Default: <code>1.e-12</code>] </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">max_it</td><td>Maximum number of linear solver iterations [Default: <code>1000</code>] </td></tr>
  </table>
  </dd>
</dl>

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          <td class="paramname"><em>p</em></td><td>)</td>
          <td></td>
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<p>Choose preconditioner for the iterative procedure. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">p</td><td>Option to choose preconditioner. See the definition of the class for available preconditioners. </td></tr>
  </table>
  </dd>
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          <td class="paramname"><em>tol</em>, </td>
        </tr>
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          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>max_it</em>&#160;</td>
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<p>Choose iteration parameters. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">tol</td><td>Tolerance for convergence of iteration process </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">max_it</td><td>Maximum number of linear solver iterations </td></tr>
  </table>
  </dd>
</dl>

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          <td>(</td>
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          <td class="paramname"><em>m</em></td><td>)</td>
          <td></td>
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<p>Choose the iterative method. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">m</td><td>Option to choose iterative solver. See the definition of the class for available iterative solvers. </td></tr>
  </table>
  </dd>
</dl>

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          <td>(</td>
          <td class="paramtype"><a class="el" href="classOFELI_1_1PETScVect.html">PETScVect</a>&lt; T_ &gt; &amp;&#160;</td>
          <td class="paramname"><em>x</em></td><td>)</td>
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<p>Solve the linear system. </p>
<p>If the member functions setIterationMethod and setPreconditioner have not been used, default methods are used </p><dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in,out]</td><td class="paramname">x</td><td>Vector containing the initial guess on input and, if convergence is achieved, the solution on output </td></tr>
  </table>
  </dd>
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          <td>(</td>
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          <td class="paramname"><em>b</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="classOFELI_1_1PETScVect.html">PETScVect</a>&lt; T_ &gt; &amp;&#160;</td>
          <td class="paramname"><em>x</em>&#160;</td>
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          <td></td>
          <td>)</td>
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<p>Solve the linear system. </p>
<p>If the member functions setIterationMethod and setPreconditioner have not been used, default methods are used </p><dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">b</td><td>Vector containing the right-hand side </td></tr>
    <tr><td class="paramdir">[in,out]</td><td class="paramname">x</td><td>Vector containing the initial guess on input and, if convergence is achieved, the solution on output </td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void checkError </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="classOFELI_1_1PETScVect.html">PETScVect</a>&lt; T_ &gt; &amp;&#160;</td>
          <td class="paramname"><em>u</em></td><td>)</td>
          <td> const</td>
        </tr>
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<p>Check residual error. </p>
<p>This function computes the residual A*x - b and outputs the number of iterations </p><dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[out]</td><td class="paramname">u</td><td>Residual vector </td></tr>
  </table>
  </dd>
</dl>

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<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">void setLSTolerances </td>
          <td>(</td>
          <td class="paramtype"><a class="el" href="group__Util.html#gaccfeb6b1e8cf41731fde610549bee67c">real_t</a>&#160;</td>
          <td class="paramname"><em>rel_tol</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="group__Util.html#gaccfeb6b1e8cf41731fde610549bee67c">real_t</a>&#160;</td>
          <td class="paramname"><em>abs_tol</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="group__Util.html#gaccfeb6b1e8cf41731fde610549bee67c">real_t</a>&#160;</td>
          <td class="paramname"><em>div_tol</em> = <code>PETSC_DEFAULT</code>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>max_it</em> = <code>PETSC_DEFAULT</code>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td> const</td>
        </tr>
      </table>
</div><div class="memdoc">

<p>Set tolerance parameters for a linear system. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir">[in]</td><td class="paramname">rel_tol</td><td>Relative convergence tolerance, relative decrease in the preconditioned residual norm </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">abs_tol</td><td>Absolute convergence tolerance of the preconditioned residual norm </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">div_tol</td><td>Divergence tolerance: Amount preconditioned residual norm </td></tr>
    <tr><td class="paramdir">[in]</td><td class="paramname">max_it</td><td>Maximum number of iterations </td></tr>
  </table>
  </dd>
</dl>

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